personalised_medicine/ALSsurv.Rnw at master · HeidiSeibold/personalised_medicine · GitHub

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\documentclass{article}
\usepackage[left=20mm, right=15mm, top=15mm, bottom=20mm]{geometry}

\begin{document}
%\VignetteEngine{knitr::knitr}
<<surv_setup>>=
library("knitr")
opts_chunk$set(cache = FALSE, echo = TRUE,
               fig.show='hold', message=FALSE, warning=FALSE)

library("ggplot2")
theme_set(theme_bw(base_size = 18))
library("partykit")
library("sandwich")
library("survival")
library("eha")
library("ggplot2")
library("plyr")
library("gridExtra")
source("basis/personalised_models.R")
source("basis/variable_importance.R")
source("basis/dependence_plots.R")
source("basis/pruning.R")


read_chunk('ALSsurv_R.R')
@


<<surv_data, cache = TRUE>>=
@

\section{Fitting function}
<<surv_fittingfunction, cache = TRUE>>=
@

\section{Compute random forest}
<<surv_forest, cache = FALSE>>=
@


\section{Obtain personalised models}
<<surv_pm, out.width = "0.99\\textwidth", out.height = "0.33\\textwidth", fig.width=12, fig.height=4>>=
@


\section{Variable importance}
<<surv_varimp>>=
@


\section{Obtain log-Likelihoods}
<<surv_logLiks, cache = FALSE>>=
@

<<surv_bootstrapLogliks>>=
@
%
%\section{Rank plot}
%<<surv_rankplot, fig.height = 11>>=
%@
%
%\section{Partial dependency plots}
%<<surv_pdplot, out.width = "0.5\\textwidth", out.height = "0.4\\textwidth">>=
%@
%
%From dependence plot make out useful variables for a model.
%<<surv_newmodel>>=
%@
%

<<surv_sessionInfo>>=
sessionInfo()
@

\end{document}